We are having images like below where we want to do the following steps:
- Automatically find all nuclei
- Classify nuclei into dividing (purple numbers) vs. non-dividing (yellow numbers)
- Measure the probability that a spatial neighbor of dividing nucleus also is dividing
Below manual annotation is not comprehensive, I just marked a few nuclei for illustration.
I think for the tasks (1) and (2) ilastik or Imaris should be very good (data actually is 3D).
My question is whether any of you knows of any standard tools that could be used to address the cell neighbor statistics aspect (3)?
Thanks a lot for your input!